My insert was also completely trashed on arrival!
I created a custom insert myself (see below image) using foam board and stick on felt from a craft shop. This is not something I would normally do but with a few google searches (Loads of people do these foam board inserts it seems!) and a couple of hours with a craft knife, cutting board and straight edge the job was done..
I still use it but it has to be said that with expansions the set quickly outgrows the space available so I now just use Ultra Pro 9 pocket card storage books from Amazon... I have 4 of them and that stores everything released so far pus enough space for a few more expansions... Its also easy to grow with another book.
Anyway, thats what I have done and I now tend to use the wooden box at home with friends as it has all the premium chips, coins etc plus hold some pre prepared decks so I can just get it out and play without any significant prep time.
Oh... an once you've done it you will find a million other uses for foam board and felt.. it really is super easy!
Good luck !